library(ggplot2)
library(dplyr)
##
## Attaching package: 'dplyr'
## The following objects are masked from 'package:stats':
##
## filter, lag
## The following objects are masked from 'package:base':
##
## intersect, setdiff, setequal, union
"%&%" = function(a,b) paste(a,b,sep="")
for(pop in c('AFA-CAU','AFA-HIS','CAU-HIS')){
res <- read.table(pop %&% '_MESA_Nk-20.local-h2_gen-corr.2017-07-21_with_SNP_count.txt',header=T)
res <- dplyr::mutate(res,min.h2=ifelse(pop1.h2<pop2.h2,pop1.h2,pop2.h2), max.h2=ifelse(pop1.h2>pop2.h2,pop1.h2,pop2.h2))
print(summary(res))
print(ggplot(res, aes(x=rG,y=pop1.h2)) + geom_point() + ggtitle(pop))
print(ggplot(res, aes(x=rG,y=pop1.se)) + geom_point() + ggtitle(pop))
print(ggplot(res, aes(x=pop1.h2,y=pop1.se)) + geom_point() + ggtitle(pop))
print(ggplot(res, aes(x=rG,y=pop2.h2)) + geom_point() + ggtitle(pop))
print(ggplot(res, aes(x=rG,y=pop2.se)) + geom_point() + ggtitle(pop))
print(ggplot(res, aes(x=pop2.h2,y=pop2.se)) + geom_point() + ggtitle(pop))
print(ggplot(res, aes(x=pop1.h2,y=pop2.h2,col=rG)) + geom_point()+scale_color_gradientn(colours = rainbow(4)) + ggtitle(pop))
print(ggplot(res, aes(x=pop1.h2,y=pop2.h2)) + stat_density_2d(aes(fill = ..level..), geom = "polygon") + ggtitle(pop))
print(ggplot(res, aes(x=pop1.h2,y=pop2.h2,col=log10(rG.se))) + geom_point() +scale_color_gradientn(colours = rainbow(4)) + ggtitle(pop))
print(ggplot(res, aes(x=rG,y=log10(rG.se),col=min.h2)) + geom_point(alpha=0.5)+scale_color_gradientn(colours = rainbow(4)) + ggtitle(pop))
print(ggplot(res, aes(x=rG,y=log10(rG.se),col=max.h2)) + geom_point(alpha=0.5)+scale_color_gradientn(colours = rainbow(4)) + ggtitle(pop))
print(ggplot(res, aes(x=rG,y=log10(rG.se))) + stat_density_2d(aes(fill = ..level..), geom = "polygon") +
coord_cartesian(xlim=c(-1,1)) + ggtitle(pop))
#keep only genes with h2>0.2 in one pop
resfilt <- dplyr::filter(res, pop1.h2 > 0.2 | pop2.h2 > 0.2)
resfilt <- dplyr::mutate(resfilt,min.h2=ifelse(pop1.h2<pop2.h2,pop1.h2,pop2.h2), max.h2=ifelse(pop1.h2>pop2.h2,pop1.h2,pop2.h2))
print(summary(resfilt))
print(ggplot(resfilt, aes(x=rG,y=log10(rG.se))) + geom_point(alpha=0.5) + ggtitle(pop))
print(ggplot(resfilt, aes(x=rG,y=log10(rG.se),col=min.h2)) + geom_point(alpha=0.5)+scale_color_gradientn(colours = rainbow(4)) + ggtitle(pop))
print(ggplot(resfilt, aes(x=rG,y=log10(rG.se),col=max.h2)) + geom_point(alpha=0.5)+scale_color_gradientn(colours = rainbow(4)) + ggtitle(pop))
print(ggplot(resfilt, aes(x=rG,y=log10(rG.se))) + stat_density_2d(aes(fill = ..level..), geom = "polygon") +
coord_cartesian(xlim=c(-1,1)) + ggtitle(pop))
print(ggplot(res, aes(x=rG,y=log10(rG.se))) + stat_density_2d(geom = "point", aes(size = ..density..), n = 20, contour = FALSE) + ggtitle(pop))
print(ggplot(res, aes(x=rG)) + geom_density() + ggtitle(pop))
print(ggplot(res, aes(x=log10(rG.se))) + geom_density() + ggtitle(pop))
print(ggplot(res, aes(x=pop1.h2)) + geom_density() + ggtitle(pop))
print(ggplot(res, aes(x=pop2.h2)) + geom_density() + ggtitle(pop))
print(ggplot(res, aes(x=rG,y=log10(rG.se))) + geom_bin2d() + ggtitle(pop))
print(ggplot(res, aes(x=rG,y=log10(rG.se),col=pop1.h2)) + geom_point() + ggtitle(pop))
print(ggplot(res, aes(x=rG,y=log10(pop1.snpcount)))+geom_point(alpha=0.5)+geom_smooth(stat="smooth") + ggtitle(pop))
print(ggplot(res, aes(x=rG,y=log10(pop2.snpcount)))+geom_point(alpha=0.5)+geom_smooth(stat="smooth") + ggtitle(pop))
cor.test(res$rG,res$pop1.snpcount,method='s')
cor.test(res$rG,res$pop2.snpcount,method='s')
}
## pop.data N ensid
## AFA-CAU_MESA_Nk-20:9797 Min. :811 ENSG00000000419.8 : 1
## 1st Qu.:811 ENSG00000000457.8 : 1
## Median :811 ENSG00000000460.12: 1
## Mean :811 ENSG00000000938.8 : 1
## 3rd Qu.:811 ENSG00000000971.11: 1
## Max. :811 ENSG00000001036.8 : 1
## (Other) :9791
## gene chr start end
## A1BG : 1 chr1 :1062 Min. : 14363 Min. : 29370
## AAAS : 1 chr19 : 752 1st Qu.: 31191920 1st Qu.: 31230667
## AACS : 1 chr2 : 657 Median : 57647548 Median : 57698944
## AAED1 : 1 chr17 : 618 Mean : 72897113 Mean : 72948622
## AAGAB : 1 chr11 : 607 3rd Qu.:108320411 3rd Qu.:108507766
## AAK1 : 1 chr3 : 584 Max. :249200395 Max. :249214145
## (Other):9791 (Other):5517
## pop1.h2 pop1.se pop2.h2 pop2.se
## Min. :0.0000 Min. :0.0046 Min. :0.0000 Min. :0.0026
## 1st Qu.:0.0051 1st Qu.:0.0524 1st Qu.:0.0052 1st Qu.:0.0203
## Median :0.0543 Median :0.0661 Median :0.0333 Median :0.0282
## Mean :0.1171 Mean :0.0663 Mean :0.1091 Mean :0.0322
## 3rd Qu.:0.1643 3rd Qu.:0.0803 3rd Qu.:0.1376 3rd Qu.:0.0441
## Max. :0.9569 Max. :0.1286 Max. :0.9802 Max. :0.0924
## NA's :570 NA's :570 NA's :570 NA's :570
## rG rG.se chrnum pop1.snpcount
## Min. :-1.0000 Min. : 0.01 Min. : 1.000 Min. : 6.0
## 1st Qu.: 0.1916 1st Qu.: 0.36 1st Qu.: 4.000 1st Qu.: 370.0
## Median : 0.9979 Median : 1.06 Median :10.000 Median : 529.0
## Mean : 0.4847 Mean : 5317.00 Mean : 9.934 Mean : 527.6
## 3rd Qu.: 1.0000 3rd Qu.: 8.93 3rd Qu.:16.000 3rd Qu.: 665.0
## Max. : 1.0000 Max. :70554.28 Max. :22.000 Max. :3065.0
## NA's :570 NA's :570
## pop2.snpcount min.h2 max.h2
## Min. : 1 Min. :0.0000 Min. :0.0000
## 1st Qu.: 319 1st Qu.:0.0029 1st Qu.:0.0141
## Median : 460 Median :0.0218 Median :0.0756
## Mean : 460 Mean :0.0843 Mean :0.1419
## 3rd Qu.: 582 3rd Qu.:0.0979 3rd Qu.:0.1965
## Max. :2728 Max. :0.9569 Max. :0.9802
## NA's :570 NA's :570
## Warning: Removed 570 rows containing missing values (geom_point).
## Warning: Removed 570 rows containing missing values (geom_point).
## Warning: Removed 570 rows containing missing values (geom_point).
## Warning: Removed 570 rows containing missing values (geom_point).
## Warning: Removed 570 rows containing missing values (geom_point).
## Warning: Removed 570 rows containing missing values (geom_point).
## Warning: Removed 570 rows containing missing values (geom_point).
## Warning: Removed 570 rows containing non-finite values (stat_density2d).
## Warning: Removed 570 rows containing missing values (geom_point).
## Warning: Removed 570 rows containing missing values (geom_point).
## Warning: Removed 570 rows containing missing values (geom_point).
## Warning: Removed 570 rows containing non-finite values (stat_density2d).
## pop.data N ensid
## AFA-CAU_MESA_Nk-20:2272 Min. :811 ENSG00000000457.8 : 1
## 1st Qu.:811 ENSG00000001084.6 : 1
## Median :811 ENSG00000001561.6 : 1
## Mean :811 ENSG00000001631.10: 1
## 3rd Qu.:811 ENSG00000002549.8 : 1
## Max. :811 ENSG00000002822.11: 1
## (Other) :2266
## gene chr start end
## AAGAB : 1 chr1 : 237 Min. : 62293 Min. : 103628
## AAR2 : 1 chr6 : 144 1st Qu.: 29686343 1st Qu.: 29748518
## AASDH : 1 chr11 : 142 Median : 58057341 Median : 58155214
## ABAT : 1 chr2 : 137 Mean : 72073652 Mean : 72128136
## ABCA7 : 1 chr19 : 135 3rd Qu.:107879509 3rd Qu.:107950688
## ABCB10 : 1 chr12 : 134 Max. :249132479 Max. :249143716
## (Other):2266 (Other):1343
## pop1.h2 pop1.se pop2.h2
## Min. :0.000017 Min. :0.01387 Min. :0.000037
## 1st Qu.:0.218694 1st Qu.:0.07684 1st Qu.:0.192619
## Median :0.293381 Median :0.08504 Median :0.292032
## Mean :0.332921 Mean :0.08363 Mean :0.328373
## 3rd Qu.:0.428686 3rd Qu.:0.09284 3rd Qu.:0.458162
## Max. :0.956931 Max. :0.12857 Max. :0.980233
##
## pop2.se rG rG.se chrnum
## Min. :0.003337 Min. :-1.0000 Min. : 0.0075 Min. : 1.000
## 1st Qu.:0.043925 1st Qu.: 0.8204 1st Qu.: 0.1021 1st Qu.: 4.000
## Median :0.051976 Median : 0.9838 Median : 0.1806 Median :10.000
## Mean :0.049661 Mean : 0.8313 Mean : 1.3737 Mean : 9.901
## 3rd Qu.:0.057356 3rd Qu.: 1.0000 3rd Qu.: 0.2853 3rd Qu.:16.000
## Max. :0.092402 Max. : 1.0000 Max. :1588.4756 Max. :22.000
##
## pop1.snpcount pop2.snpcount min.h2 max.h2
## Min. : 57.0 Min. : 50.0 Min. :0.000017 Min. :0.2001
## 1st Qu.: 427.0 1st Qu.: 368.0 1st Qu.:0.125627 1st Qu.:0.2617
## Median : 572.0 Median : 499.5 Median :0.220588 Median :0.3496
## Mean : 571.9 Mean : 500.3 Mean :0.262645 Mean :0.3986
## 3rd Qu.: 705.0 3rd Qu.: 618.0 3rd Qu.:0.360196 3rd Qu.:0.5013
## Max. :1486.0 Max. :1268.0 Max. :0.956931 Max. :0.9802
##
## Warning: Removed 570 rows containing non-finite values (stat_density2d).
## Warning: Removed 570 rows containing non-finite values (stat_density).
## Warning: Removed 570 rows containing non-finite values (stat_density).
## Warning: Removed 570 rows containing non-finite values (stat_density).
## Warning: Removed 570 rows containing non-finite values (stat_density).
## Warning: Removed 570 rows containing non-finite values (stat_bin2d).
## Warning: Removed 570 rows containing missing values (geom_point).
## `geom_smooth()` using method = 'gam'
## Warning: Removed 570 rows containing non-finite values (stat_smooth).
## Warning: Removed 570 rows containing missing values (geom_point).
## `geom_smooth()` using method = 'gam'
## Warning: Removed 570 rows containing non-finite values (stat_smooth).
## Warning: Removed 570 rows containing missing values (geom_point).
## Warning in cor.test.default(res$rG, res$pop1.snpcount, method = "s"):
## Cannot compute exact p-value with ties
## Warning in cor.test.default(res$rG, res$pop2.snpcount, method = "s"):
## Cannot compute exact p-value with ties
## pop.data N ensid
## AFA-HIS_MESA_Nk-20:9797 Min. :585 ENSG00000000419.8 : 1
## 1st Qu.:585 ENSG00000000457.8 : 1
## Median :585 ENSG00000000460.12: 1
## Mean :585 ENSG00000000938.8 : 1
## 3rd Qu.:585 ENSG00000000971.11: 1
## Max. :585 ENSG00000001036.8 : 1
## (Other) :9791
## gene chr start end
## A1BG : 1 chr1 :1062 Min. : 14363 Min. : 29370
## AAAS : 1 chr19 : 752 1st Qu.: 31191920 1st Qu.: 31230667
## AACS : 1 chr2 : 657 Median : 57647548 Median : 57698944
## AAED1 : 1 chr17 : 618 Mean : 72897113 Mean : 72948622
## AAGAB : 1 chr11 : 607 3rd Qu.:108320411 3rd Qu.:108507766
## AAK1 : 1 chr3 : 584 Max. :249200395 Max. :249214145
## (Other):9791 (Other):5517
## pop1.h2 pop1.se pop2.h2 pop2.se
## Min. :0.0000 Min. :0.0092 Min. :0.0000 Min. :0.0050
## 1st Qu.:0.0059 1st Qu.:0.0511 1st Qu.:0.0061 1st Qu.:0.0361
## Median :0.0549 Median :0.0641 Median :0.0521 Median :0.0483
## Mean :0.1168 Mean :0.0645 Mean :0.1270 Mean :0.0495
## 3rd Qu.:0.1624 3rd Qu.:0.0782 3rd Qu.:0.1778 3rd Qu.:0.0635
## Max. :0.8738 Max. :0.1286 Max. :0.9217 Max. :0.1022
## NA's :528 NA's :528 NA's :528 NA's :528
## rG rG.se chrnum pop1.snpcount
## Min. :-1.0000 Min. : 0.01 Min. : 1.000 Min. : 6.0
## 1st Qu.: 0.5667 1st Qu.: 0.34 1st Qu.: 4.000 1st Qu.: 370.0
## Median : 1.0000 Median : 1.08 Median :10.000 Median : 529.0
## Mean : 0.5744 Mean : 7249.01 Mean : 9.934 Mean : 527.6
## 3rd Qu.: 1.0000 3rd Qu.: 9.59 3rd Qu.:16.000 3rd Qu.: 665.0
## Max. : 1.0000 Max. :84785.94 Max. :22.000 Max. :3065.0
## NA's :528 NA's :528
## pop2.snpcount min.h2 max.h2
## Min. : 6.0 Min. :0.0000 Min. :0.0000
## 1st Qu.: 370.0 1st Qu.:0.0033 1st Qu.:0.0159
## Median : 529.0 Median :0.0287 Median :0.0826
## Mean : 528.4 Mean :0.0957 Mean :0.1481
## 3rd Qu.: 667.0 3rd Qu.:0.1224 3rd Qu.:0.2102
## Max. :3054.0 Max. :0.8738 Max. :0.9217
## NA's :528 NA's :528
## Warning: Removed 528 rows containing missing values (geom_point).
## Warning: Removed 528 rows containing missing values (geom_point).
## Warning: Removed 528 rows containing missing values (geom_point).
## Warning: Removed 528 rows containing missing values (geom_point).
## Warning: Removed 528 rows containing missing values (geom_point).
## Warning: Removed 528 rows containing missing values (geom_point).
## Warning: Removed 528 rows containing missing values (geom_point).
## Warning: Removed 528 rows containing non-finite values (stat_density2d).
## Warning: Removed 528 rows containing missing values (geom_point).
## Warning: Removed 528 rows containing missing values (geom_point).
## Warning: Removed 528 rows containing missing values (geom_point).
## Warning: Removed 528 rows containing non-finite values (stat_density2d).
## pop.data N ensid
## AFA-HIS_MESA_Nk-20:2452 Min. :585 ENSG00000000457.8 : 1
## 1st Qu.:585 ENSG00000001084.6 : 1
## Median :585 ENSG00000001561.6 : 1
## Mean :585 ENSG00000001631.10: 1
## 3rd Qu.:585 ENSG00000002549.8 : 1
## Max. :585 ENSG00000002822.11: 1
## (Other) :2446
## gene chr start end
## AAGAB : 1 chr1 : 255 Min. : 96407 Min. : 103628
## AASDH : 1 chr6 : 157 1st Qu.: 29755679 1st Qu.: 29901554
## ABAT : 1 chr2 : 151 Median : 58223710 Median : 58234066
## ABCA7 : 1 chr11 : 150 Mean : 72229107 Mean : 72282598
## ABCB10 : 1 chr19 : 147 3rd Qu.:108838558 3rd Qu.:108863164
## ABCC3 : 1 chr12 : 146 Max. :249104650 Max. :249120832
## (Other):2446 (Other):1446
## pop1.h2 pop1.se pop2.h2 pop2.se
## Min. :0.000097 Min. :0.02457 Min. :0.000094 Min. :0.01511
## 1st Qu.:0.203427 1st Qu.:0.07368 1st Qu.:0.225010 1st Qu.:0.06202
## Median :0.281652 Median :0.08202 Median :0.318536 Median :0.06906
## Mean :0.317939 Mean :0.08082 Mean :0.358031 Mean :0.06670
## 3rd Qu.:0.414189 3rd Qu.:0.08926 3rd Qu.:0.467325 3rd Qu.:0.07415
## Max. :0.873794 Max. :0.11604 Max. :0.921703 Max. :0.10223
##
## rG rG.se chrnum pop1.snpcount
## Min. :-1.0000 Min. : 0.01333 Min. : 1.000 Min. : 57
## 1st Qu.: 0.9123 1st Qu.: 0.09989 1st Qu.: 4.000 1st Qu.: 429
## Median : 1.0000 Median : 0.17433 Median : 9.000 Median : 572
## Mean : 0.9075 Mean : 0.46734 Mean : 9.842 Mean : 571
## 3rd Qu.: 1.0000 3rd Qu.: 0.27529 3rd Qu.:15.250 3rd Qu.: 703
## Max. : 1.0000 Max. :217.88082 Max. :22.000 Max. :1486
##
## pop2.snpcount min.h2 max.h2
## Min. : 59.0 Min. :0.000094 Min. :0.2001
## 1st Qu.: 427.8 1st Qu.:0.152918 1st Qu.:0.2617
## Median : 573.0 Median :0.241634 Median :0.3520
## Mean : 571.8 Mean :0.281497 Mean :0.3945
## 3rd Qu.: 705.0 3rd Qu.:0.375367 3rd Qu.:0.4865
## Max. :1480.0 Max. :0.873794 Max. :0.9217
##
## Warning: Removed 528 rows containing non-finite values (stat_density2d).
## Warning: Removed 528 rows containing non-finite values (stat_density).
## Warning: Removed 528 rows containing non-finite values (stat_density).
## Warning: Removed 528 rows containing non-finite values (stat_density).
## Warning: Removed 528 rows containing non-finite values (stat_density).
## Warning: Removed 528 rows containing non-finite values (stat_bin2d).
## Warning: Removed 528 rows containing missing values (geom_point).
## `geom_smooth()` using method = 'gam'
## Warning: Removed 528 rows containing non-finite values (stat_smooth).
## Warning: Removed 528 rows containing missing values (geom_point).
## `geom_smooth()` using method = 'gam'
## Warning: Removed 528 rows containing non-finite values (stat_smooth).
## Warning: Removed 528 rows containing missing values (geom_point).
## Warning in cor.test.default(res$rG, res$pop1.snpcount, method = "s"):
## Cannot compute exact p-value with ties
## Warning in cor.test.default(res$rG, res$pop2.snpcount, method = "s"):
## Cannot compute exact p-value with ties
## pop.data N ensid
## CAU-HIS_MESA_Nk-20:9797 Min. :930 ENSG00000000419.8 : 1
## 1st Qu.:930 ENSG00000000457.8 : 1
## Median :930 ENSG00000000460.12: 1
## Mean :930 ENSG00000000938.8 : 1
## 3rd Qu.:930 ENSG00000000971.11: 1
## Max. :930 ENSG00000001036.8 : 1
## (Other) :9791
## gene chr start end
## A1BG : 1 chr1 :1062 Min. : 14363 Min. : 29370
## AAAS : 1 chr19 : 752 1st Qu.: 31191920 1st Qu.: 31230667
## AACS : 1 chr2 : 657 Median : 57647548 Median : 57698944
## AAED1 : 1 chr17 : 618 Mean : 72897113 Mean : 72948622
## AAGAB : 1 chr11 : 607 3rd Qu.:108320411 3rd Qu.:108507766
## AAK1 : 1 chr3 : 584 Max. :249200395 Max. :249214145
## (Other):9791 (Other):5517
## pop1.h2 pop1.se pop2.h2 pop2.se
## Min. :0.0000 Min. :0.0011 Min. :0.0000 Min. :0.0041
## 1st Qu.:0.0051 1st Qu.:0.0204 1st Qu.:0.0045 1st Qu.:0.0305
## Median :0.0363 Median :0.0280 Median :0.0433 Median :0.0411
## Mean :0.1068 Mean :0.0314 Mean :0.1130 Mean :0.0432
## 3rd Qu.:0.1341 3rd Qu.:0.0421 3rd Qu.:0.1502 3rd Qu.:0.0563
## Max. :0.9786 Max. :0.0864 Max. :0.9834 Max. :0.0941
## NA's :317 NA's :317 NA's :317 NA's :317
## rG rG.se chrnum pop1.snpcount
## Min. :-1.0000 Min. : 0.00 Min. : 1.000 Min. : 1
## 1st Qu.: 0.7060 1st Qu.: 0.21 1st Qu.: 4.000 1st Qu.: 319
## Median : 1.0000 Median : 0.76 Median :10.000 Median : 460
## Mean : 0.6217 Mean : 3859.83 Mean : 9.934 Mean : 460
## 3rd Qu.: 1.0000 3rd Qu.: 6.33 3rd Qu.:16.000 3rd Qu.: 582
## Max. : 1.0000 Max. :54431.91 Max. :22.000 Max. :2728
## NA's :317 NA's :317
## pop2.snpcount min.h2 max.h2
## Min. : 6.0 Min. :0.0000 Min. :0.0000
## 1st Qu.: 370.0 1st Qu.:0.0026 1st Qu.:0.0120
## Median : 529.0 Median :0.0231 Median :0.0573
## Mean : 528.4 Mean :0.0925 Mean :0.1273
## 3rd Qu.: 667.0 3rd Qu.:0.1113 3rd Qu.:0.1716
## Max. :3054.0 Max. :0.9786 Max. :0.9834
## NA's :317 NA's :317
## Warning: Removed 317 rows containing missing values (geom_point).
## Warning: Removed 317 rows containing missing values (geom_point).
## Warning: Removed 317 rows containing missing values (geom_point).
## Warning: Removed 317 rows containing missing values (geom_point).
## Warning: Removed 317 rows containing missing values (geom_point).
## Warning: Removed 317 rows containing missing values (geom_point).
## Warning: Removed 317 rows containing missing values (geom_point).
## Warning: Removed 317 rows containing non-finite values (stat_density2d).
## Warning: Removed 317 rows containing missing values (geom_point).
## Warning: Removed 317 rows containing missing values (geom_point).
## Warning: Removed 317 rows containing missing values (geom_point).
## Warning: Removed 317 rows containing non-finite values (stat_density2d).
## pop.data N ensid
## CAU-HIS_MESA_Nk-20:2051 Min. :930 ENSG00000001561.6 : 1
## 1st Qu.:930 ENSG00000002822.11: 1
## Median :930 ENSG00000002933.3 : 1
## Mean :930 ENSG00000003056.3 : 1
## 3rd Qu.:930 ENSG00000003393.10: 1
## Max. :930 ENSG00000003402.14: 1
## (Other) :2045
## gene chr start end
## AAGAB : 1 chr1 : 207 Min. : 62293 Min. : 103628
## AAR2 : 1 chr11 : 134 1st Qu.: 28348054 1st Qu.: 28562072
## AASDH : 1 chr6 : 134 Median : 57994127 Median : 58154136
## ABAT : 1 chr19 : 127 Mean : 71868524 Mean : 71920540
## ABCA7 : 1 chr17 : 122 3rd Qu.:107995865 3rd Qu.:108072570
## ABCC3 : 1 chr7 : 120 Max. :247581351 Max. :247612119
## (Other):2045 (Other):1207
## pop1.h2 pop1.se pop2.h2
## Min. :0.000146 Min. :0.003304 Min. :0.001276
## 1st Qu.:0.218156 1st Qu.:0.045296 1st Qu.:0.235171
## Median :0.312824 Median :0.050967 Median :0.320943
## Mean :0.353212 Mean :0.049529 Mean :0.368179
## 3rd Qu.:0.470564 3rd Qu.:0.055119 3rd Qu.:0.470548
## Max. :0.978634 Max. :0.086425 Max. :0.983391
##
## pop2.se rG rG.se chrnum
## Min. :0.004056 Min. :-1.0000 Min. : 0.00234 Min. : 1.000
## 1st Qu.:0.058120 1st Qu.: 0.9540 1st Qu.: 0.04368 1st Qu.: 5.000
## Median :0.063636 Median : 1.0000 Median : 0.08111 Median :10.000
## Mean :0.062446 Mean : 0.9463 Mean : 0.14746 Mean : 9.975
## 3rd Qu.:0.068726 3rd Qu.: 1.0000 3rd Qu.: 0.12859 3rd Qu.:16.000
## Max. :0.094097 Max. : 1.0000 Max. :69.73787 Max. :22.000
##
## pop1.snpcount pop2.snpcount min.h2 max.h2
## Min. : 50.0 Min. : 59.0 Min. :0.000146 Min. :0.2001
## 1st Qu.: 365.0 1st Qu.: 424.0 1st Qu.:0.188851 1st Qu.:0.2564
## Median : 496.0 Median : 570.0 Median :0.275619 Median :0.3511
## Mean : 498.7 Mean : 569.9 Mean :0.322138 Mean :0.3993
## 3rd Qu.: 619.5 3rd Qu.: 704.0 3rd Qu.:0.432113 3rd Qu.:0.5011
## Max. :1268.0 Max. :1480.0 Max. :0.978634 Max. :0.9834
##
## Warning: Removed 317 rows containing non-finite values (stat_density2d).
## Warning: Removed 317 rows containing non-finite values (stat_density).
## Warning: Removed 317 rows containing non-finite values (stat_density).
## Warning: Removed 317 rows containing non-finite values (stat_density).
## Warning: Removed 317 rows containing non-finite values (stat_density).
## Warning: Removed 317 rows containing non-finite values (stat_bin2d).
## Warning: Removed 317 rows containing missing values (geom_point).
## `geom_smooth()` using method = 'gam'
## Warning: Removed 317 rows containing non-finite values (stat_smooth).
## Warning: Removed 317 rows containing missing values (geom_point).
## `geom_smooth()` using method = 'gam'
## Warning: Removed 317 rows containing non-finite values (stat_smooth).
## Warning: Removed 317 rows containing missing values (geom_point).
## Warning in cor.test.default(res$rG, res$pop1.snpcount, method = "s"):
## Cannot compute exact p-value with ties
## Warning in cor.test.default(res$rG, res$pop2.snpcount, method = "s"):
## Cannot compute exact p-value with ties
